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Adam Cribbs
I lead a computational biology team with a broad interest in systems biology, immunology and epigenetics. My group is also heavily focused on developing novel multiplexed single-cell technology. Using this technology, our goal is to understand how cellular heterogeneity encodes epigenetic function and regulation in complex biological systems.
I am responsible for running a number of computational single-cell projects, of which the Tendon Seed Network, part of the Human Cell Atlas (HCA), is the largest. The aim of the Tendon Seed Network is to develop clinical, biological and computational single-cell sequencing workflows to investigate the cell composition of tendon. Specifically, using spatial transcriptomics, imaging and single-cell nuclear RNA-seq we are building the worlds first map of the healthy Human tendon. This project is one of only two HCA initiatives established within the University of Oxford, and the only UK based Chan Zuckerberg Initiative (CZI) funded scheme.
My background is as a molecular immunologist, having completed a Ph.D. at Imperial College London in May 2013. Following a brief wet-lab postdoctoral position within the Oppermann group, University of Oxford, I undertook a highly competitive 3 year MRC Fellowship in Computational Biology (at the Computational Genomics and Training Centre (CGAT)), also at the University of Oxford.
As a result of my extensive computational training at CGAT, I have developed a number of core competencies in statistics, mathematics and software development, enabling the difficult analysis and interpretation of next-generation sequencing data. Following the completion of my fellowship I was appointed group leader in systems biology at the Botnar research Centre, University of Oxford.
Education/Employment
Group Leader in Systems Biology
University of Oxford
Botnar Research Centre
present - 2018
- Managing a team of 2 computational postdoctoral researchers and supervising two Dphil students
MRC Career Development Fellowship in Computational Biology
University of Oxford
N/A
2018 - 2015
- Development of computational biology skills for next-generation sequencing and big data analysis.
- Collaborative projects with researchers throughout the University of Oxford.
Junior Research Fellowship (JRF)
University of Oxford
Campion hall
2018 - 2016
- Provided financial support to attend conferences and purchase training resources.
- Have developed collaborative links in ethical studies that has resulted in a publication: “Ethical considerations regarding genome editing and its inheritance”.
Postdoctoral Scientist in Immunology & Epigenetics
University of Oxford
Botnar Research Centre
2015 - 2013
- Investigating the epigenetics of NK cells and T cells in rheumatoid arthritis
- Supervised by Professor Sir Marc Feldmann and Professor Udo Oppermann
PhD in Molecular T Cell Immunology
Imperial College London
Kennedy Institute of Rheumatology
2013 - 2009
- Thesis: The molecular mechsnism of defective regulatory T cell function in Rheumatoid Arthritis
- Supported by a highly competitive studentship from the Kennedy Arthritis Trust.
Funding
The Tendon Seed Network (Part of the Human Cell Atlas) - £1,500,000
Co-applicant
ChanZuckerberg Initiative
2022 - 2019
Understanding the epigenetic mechanisms of chemotherapy resistance in medulloblastoma - £ 111,000
Oxford lead
The Royal Society
2022 - 2019
Advanced Oligonucleotide Capture Beads - £369,362
Co-applicant
UK Innovation
2021 - 2020
Therapeutic targeting and understanding of oncogenic driver networks in chordoma
Lead
BCRT
2021 - 2019
Investigating epigenetic heterogeneity using single cell RNA-seq in multiple myeloma - £15,000
Lead
CRUK Oxford Development Fund (AstraZeneca supported)
2020 - 2019
Transcriptional development of human primary osteocytes in a 3D bone organ - £25,382
Co-applicant
Organ-on-a-chip
2020 - 2019
Patents
Biomarkers and their uses thereof in diagnosing pre-eclampsia
N/A
N/A
2018
- Application number GB1806042.6
The diagnosis of rheumatoid arthritis using DNA methylation
N/A
N/A
2014
- Application number GB1400248.9
- Sole inventor
Multiplexed single-cell droplet based technolgies
N/A
N/A
N/A
- In progress. Patent being handled by JA Kemp
Publications
Histone H3K27me3 demethylases regulate human Th17 cell development and effector functions by impacting on metabolism
Adam P Cribbs, Stefan Terlecki-Zaniewicz, Martin Philpott, Jeroen Baardman, David Ahern, Morten Lindow, Susanna Obad, Henrik Oerum, Brant Sampey, Palwinder K Mander, Henry Penn, Paul Wordsworth, Paul Bowness, Menno de Winther, Rab K Prinjha, Marc Feldmann and Udo Oppermann. PNAS
N/A
2020
An ontogenetic switch drives the positive and negative selection of B cells
Xijin Xu, Mukta Deobagkar-Lele, Katherine R Bull, Tanya L: Cockford, Adam J Mead, Adam P Cribbs, David Sims, Consuelo Anzilotti and Richard Cornall. PNAS
N/A
2020
Mass cytometry analysis reveals a distinct immune environment in peritoneal fluid in endometriosis: a characterisation study
Guo M, Bafligil C, Tapmeier T, Manek S, Shang C, Martinez F, Schmidt N, Obendorf M, Hess-Stumpp H, Zollner T, Kennedy S, Becker C, Zondervan K, Cribbs AP* and Oppermann U. BMC Medicine. *Senior corresponding author
N/A
2020
A Chemical Probe for Tudor Domain Protein Spindlin1 to Investigate Chromatin Function
Vincent Fagan, Catrine Johansson, Carina Gileadi, Octovia Monteiro, James E Dunford, Reshma Nibhani, Martin Philpott, Jessica Malzahn, Graham Wells, Ruth Faram, Adam P C ribbs, Nadia Halidi, Fengling Li, Irene Chau, Holger Greschnik, Sirkannathasan Velupillai, Adellah Allali-Hassani, James Bennett, Thomas Christott, Charline Giroud, Andrew Lewis, Kilian V M Huber, Nick Athanasou, Chas Bountra, Manfred Jung, Roland Schule, Masoud Vedadi, Cheryl Arrowsmith, Yan Xiong, Jian Jin, Oleg Fedorov, Gillian Farnie, Paul E Brennan and Udo Oppermann. J Med Chem
N/A
2019
Maternal circulating syncytiotrophoblast-derived extracellular vesicles contain biologically active 5’-tRNA halves
William R Cooke, Adam P Cribbs, Wei Zhang, Neva Kandzija, Carolina Motta-Mejia, Eszter Dombi, Rannya Ria Ana, Sofia Cerdeira, Christopher Redman and Manu Vatish. Biochem Biophys Res Commun
N/A
2019
CGAT-core, a python framework for building scalable, reproducible computational biology workflows.
Adam P. Cribbs, Sebastian Luna-Valero, Charlotte George, Ian M. Sudbery, Antonio J. Berlanga-Taylor, Stephen N. Sansom, Tom Smith, Nicholas E. Ilott, Jethro Johnson, Jakub Scaber, Katherine Brown, David Sims, Andreas Heger. F1000 Research
N/A
2019
Bromodomain inhibition of the coactivators CBP/EP300 facilitates cellular reprogramming.
Ayyub Ebrahimi, Kenan Sevin , Glben Grhan Sevin , Adam Cribbs , Martin Philpott , Frat Uyulur , Tunc Morova , James Dunford , Sencer Gklemez , _ule Ar , Udo Oppermann. Nature Chemical Biology
N/A
2019
Human immunodeficiency reveals the Zn2+-dependence of B cell development
Consuelo Anzilotti , David Swan , Bertrand Boisson , Mukta Deobagkar-Lele , Pauline Chabosseau , Karin Engelhardt , Xijin Xu , Katherine Bull , Eleanor Cawthorne , Adam Cribbs , Ms. Tanya Crockford , Tarana Dang , Amy Fearn , Emma Fenech , Sarah de Jong , Dr. Cindy Ma , David Sims , Yaobo Xu , Andrew Cant, Gary Kleiner , T Leahy , M de la Morena , Jennifer Puck , Ralph Shapiro , Mirjam van der Burg , John Christianson , Benjamin Davies , John McGrath , Stefan Przyborski , Guy Rutter , Mauro Santibanez Koref , Prof. Stuart Tangye , Andreas Werner , Jean-Laurent Casanova , Richard Cornall , Mary Ellen Conley. Nature Immunology
N/A
2019
Design and characterisation of covalent inhibitors of KDM5.
Saleta Vazquez-Rodriguez; Miranda Wright; Catherine M. Rogers; Adam Cribbs; Srikannathasan Velupillai; Martin Philpott; Henry Lee; James E Dunford; Kilian V. M. Huber; Mathew B. Robers; James D. Vasta; Marie Laetitia Thezenas; Sarah Bonham; Benedikt Kessler; James Bennett; Oleg Fedorov; Florence Raynaud; Adam Donovan; Julian Blagg; Vassilios Bavetsias; Udo Oppermann; Akane Kawamura; Paul Brennan. Angewandte Chemie
N/A
2018
Invasive Nontyphoidal salmonella exploits divergent immune evasion strategies in infected and bystander dendritic cells
Anna Aulicino, Kevin Rue-Albrecht, Lorena Preciado-Llanes, Giorgio Napolitani, Neil Ashley, Tim Ambrose, Adam Cribbs, Melita Gordon, David Sims, Alison Simmons. Nature Immunology
N/A
2018
Ethical considerations regarding genome editing and its inheritance
Adam P Cribbs and Sumeth Perera
N/A
2017
Production and concentration of lentivirus for transduction of primary T cells
Alan Kennedy and Adam P Cribbs. Lentiviral vectors and exosomes as gene and protein delivery tools. Spinger
N/A
2016
The role of kynuernine pathway in inflammatory disease.
Adam P cribbs and Richard Williams. Spinger
N/A
2015
Indoleamine 2,3-dioxygenase-1 is protective in atherosclerosis and its metabolites provide new opportunities for drug development
Jennifer E Cole, Nagore Astola, Adam P Cribbs, Micheal E Goddard, Inhye Park, Patricia Green, Alun H Davies, Richard O Williams, Marc Feldmann and Claudia Monaco. PNAS
N/A
2015
Understanding the role of DNA methylation in rheumatoid arthritis - therapeutic and diagnostic implications
Adam P cribbs, Marc Feldmann and Udo Oppermann. Therapeutic advances in musculoskeletal diseases
N/A
2015
Methotrexate restores regulatory T cell function through demethylation of the foxp3 upstream enhancer in patients with rheumatoid arthritis.
Adam P Cribbs, Alan Kennedy, Henry Penn, Parisa Amjadi, Patricia Green, Khaja Syed, Bernard Gregory Fionula M. Brennan and Richard O. Williams. Arthritis & Rheumatism
N/A
2015
Hypomethylation of an upstream enhancer in the Foxp3 locus correlates with elevated gene expression in human regulatory T cells
Alan Kennedy, Emily M. Schmidt, Adam P. Cribbs, Henry Penn, Parisa Amjadi, Khaja Syed, Jordan E. Read, Patricia Green, Bernard Gregory and Fionula M. Brennan. European Journal of Immunology
N/A
2014
Defective regulatory T cells in rheumatoid arthritis fail to activate IDO due to methylation of an NFAT binding site within the CTLA-4 promoter
Adam P Cribbs, Alan Kennedy, Jordan E. Read, Parisa Amjadi, Patricia Green, Henry Penn, Khaja Syed, Szymon W. Manka, Bernard Gregory Fionula M. Brennan and Richard O. Williams. Arthritids & Rheumatology. Research highlight in Nature Reviews Rheumatology
N/A
2014
Resistance to regulatory T cell-mediated suppression in rheumatoid arthritis can be bypassed by ectopic foxp3 expression in pathogenic synovial cells.
Paul A Beavis, Bernard Gregory, Patricia Green, Adam P Cribbs, Alan Kennedy, Parisa Amjadi, Andrew C Palfreeman, Marc Feldmann and Fionula Brennan. PNAS
N/A
2011